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Stromatolites are complex lithified structures with a well-defined layered structure thought to have been formed by trapping and binding of sediment particles by micro-organisms, especially cyanobacteria. Modern marine stromatolites in the Bahamas live in a high-energy environment (surf zone) and are regularly buried by moving sands. We investigated stromatolite cyanobacterial photophysiology ex situ, during and after sand burial using variable fluorescence studies. Buried samples inactivated their photosynthetic electron transport, but only when oxygen concentrations decreased to low levels. Post-burial, the stromatolite cyanobacterial community reactivated its photosynthetic activity within 1 to 2 h, but this activation was light dependent. It is therefore speculated that the redox state of the plastoquinone pool determines the inactivation/reactivation processes. The ability of cyanobacteria to survive and recover from burial by sediment could be a fundamental attribute that has contributed to the success of cyanobacteria as stromatolite builders and for the actual existence of stromatolites as organo-sedimentary structures with a putative presence spanning 3500 million yr.